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LOC126862652 BRD4-independent group 4 enhancer GRCh37_chr17:75466846-75468045 [ Homo sapiens (human) ]

Gene ID: 126862652, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862652
Gene description
BRD4-independent group 4 enhancer GRCh37_chr17:75466846-75468045
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA). In HCT116 colorectal carcinoma cells, a subregion was defined as a group 4 enhancer that depends on the BRD2, P300/CBP, MED14 and CDK7 cofactors, but it has limited or no dependence on the BRD4 bromodomain protein. Another subregion was also validated as an enhancer by ChIP-STARR-seq in primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (77470764..77472556)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (78364464..78366256)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene septin 9 Neighboring gene uncharacterized LOC112268198 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75443411-75443911 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:75445010-75445917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:75445918-75446824 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:75446825-75447732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12841 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:75448639-75449546 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75450454-75451360 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75451361-75452267 Neighboring gene uncharacterized LOC105371903 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75452917-75453530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75453531-75454145 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:75455989-75456602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:75456603-75457216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12846 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12847 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:75462088-75462839 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:75462840-75463592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:75464738-75465290 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:75468633-75469338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75470024-75470524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75470525-75471025 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:75471103-75471943 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:75492509-75493058 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:75493059-75493606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75498470-75498970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75523708-75524208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75524209-75524709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75531141-75531642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75531643-75532142 Neighboring gene uncharacterized LOC400622 Neighboring gene uncharacterized LOC100507351 Neighboring gene uncharacterized LOC124904103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75559446-75559946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75559947-75560447

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 12849
  • ATAC-STARR-seq lymphoblastoid active region 12850
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:75467925-75468632

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_087149.3 

    Range
    101..1893
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    77470764..77472556
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    78364464..78366256
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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